Needing a bigger magnifying glass

The HiP-CT technique got its start as two German pathologists raced to track the SARS-CoV-2 virus’s punishing effects across the human body.
As soon as news of unusual pneumonia cases began trickling out of China, Danny Jonigk—a thoracic diseases pathologist at Hannover Medical School—and Maximilian Ackermann, a pathologist at University Medical Center Mainz, were on high alert. Both had expertise in lung disease, and right away they knew COVID-19 was unusual. The two were especially concerned about reports of a “silent hypoxia” that left COVID-19 patients awake but caused their blood oxygen levels to plummet.
Ackermann and Jonigk suspected that SARS-CoV-2 was somehow attacking the lungs’ blood vessels. As the disease spread through Germany in March 2020, the duo began conducting autopsies of COVID-19 victims. They soon tested their blood-vessel hypothesis by injecting tissue samples with resin and then dissolving the tissues in acid, which left behind faithful casts of the original vasculature.
Using this technique, Ackermann and Jonigk compared the tissues of people who hadn’t died of COVID-19 with those who had. They immediately saw that among COVID-19 victims, the smallest blood vessels in the lungs were distorted and reshaped. These landmark results, published online in May 2020, showed that COVID-19 wasn’t strictly a respiratory disease but a vascular one—one that could affect organs across the entire body.
“If you go through the human body and you take all the blood vessels in one line, you come up with [60,000] to 70,000 miles, double the distance around the Equator,” says Ackermann, who is also a pathologist at Wuppertal, Germany’s HELIO Clinics. If just one percent of these blood vessels gets attacked by a virus, he adds, the blood’s flow and ability to absorb oxygen can be impaired, with potentially devastating consequences across entire organs.
As soon as they recognized COVID-19’s vascular effects, Jonigk and Ackermann realized that they needed a much better view of the damage.
Medical x-rays such as CT scans can provide a view of an entire organ, but they weren’t high-resolution enough. Biopsies can let scientists study tissue samples under a microscope, but the resulting images are only small bits of a whole organ and can’t show how COVID-19 progresses across an entire lung. And the team’s resin technique required dissolving tissue, which destroys the sample and limits further study.
“At the end of the day, [the] lung is oxygen in, carbon dioxide out—but for that, it has thousands and thousands of miles of blood vessels and capillaries that are so finely and nicely arranged … it’s almost a miracle,” says Jonigk, the founding principal investigator of the German Center of Lung Research. “So how could we actually assess something as complex as COVID-19 … without destroying the organ?”
Jonigk and Ackermann needed the unprecedented: a series of x-rays, all done on the same organ, that would let researchers zoom into portions of the organ down to the cellular scale. In March 2020, the German duo reached out to a longtime collaborator of theirs, Peter Lee, a materials scientist and chair of emerging technologies at UCL. Lee‘s specialty is studying biological materials with powerful x-rays—so his mind immediately went to the French Alps.

Getting the scans to work

The European Synchrotron Radiation Facility sits in the northwestern corner of Grenoble on a triangular plot of land where two rivers meet. The facility is a particle accelerator that makes electrons travel at nearly the speed of light around a half-mile-long circular track. As these electrons careen round and round, powerful magnets along the track bend the particle stream, which causes the electrons to emit the world’s brightest x-rays.
This powerful radiation lets the ESRF peer into objects at the scale of micrometers, even nanometers. It is frequently used to study materials such as alloys and composites, check the molecular structures of proteins, and even reconstruct ancient fossils without having to separate rock from bone. Ackermann, Jonigk, and Lee wanted to use this huge instrument to perform the world’s most detailed x-ray scans of a human organ.
Enter Tafforeau, whose work at the ESRF has stretched the limits of what synchrotron scans can see. His impressive bag of tricks previously let scientists peer inside dinosaur eggs and virtually unwrap mummies, and almost immediately, Tafforeau confirmed that the synchrotron could, in theory, make a good scan of an entire lung lobe. But actually scanning a whole human organ posed a grand challenge.
For one, there’s the issue of contrast. Standard x-rays make images based on how much radiation gets absorbed by different materials, with heavier elements absorbing more than lighter ones. Soft tissues are mostly made of light elements—carbon, hydrogen, oxygen, and so on—which is why they don’t show up clearly in a classic medical x-ray.
One of the ESRF’s great benefits is that its x-ray beams are very coherent: Light moves in waves, and in the ESRF’s case, its x-rays all start out with the same frequency and alignment, undulating in unison like the marks left behind by a zen garden’s rake. But as these x-rays move through an object, subtle differences in density can cause each x-ray’s path to deviate slightly, a difference that gets more detectable the farther the x-rays propagate once they exit the object. These deviations can reveal the slight density differences within an object, even if it is made of light elements.
But stability is another challenge. To pull off a series of zoomed-in x-rays, a given organ would have to be immobilized in its natural shape so it wouldn’t flex and shift by more than a thousandth of a millimeter. Any more wiggle than that, and successive x-ray scans on the same organ wouldn’t align with each other. Needless to say, though, organs can be quite floppy.
Lee and his team at UCL rushed to devise containers that could withstand the synchrotron’s x-rays but also let through as many waves as possible. Lee also juggled the project’s overall organization—such as the finer points of shipping human organs between Germany and France—and recruited Walsh, who specializes in huge biomedical datasets, to help work out how to analyze the scans. Back in France, Tafforeau’s jobs included refining the scanning procedure and figuring out how to keep the organs still within the containers that Lee’s team was building.

Tackling future challenges

The team published its first full description of the HiP-CT method in November 2021, and the researchers also have published a detailed look at how COVID-19 affects certain kinds of blood circulation in the lungs.
The scans also yielded an unanticipated bonus: helping the researchers convince friends and relatives to get vaccinated. In severe COVID-19 cases, many of the lungs’ blood vessels look dilated and bloated, and at smaller scales, abnormal bundles of tiny blood vessels form.
“When you see the structure of lungs of people who die from COVID, it does not look like lungs—it’s a big mess,” Tafforeau says.
Even in healthy organs, he adds, the scans were revealing subtle anatomical features that had never been documented because nobody has ever seen a human organ in this level of detail before. With more than a million dollars in funding from the Chan Zuckerberg Initiative—a nonprofit founded by Facebook CEO Mark Zuckerberg and physician Priscilla Chan, Zuckerberg’s wife—the HiP-CT team is now creating what it’s calling the Human Organ Atlas.
So far, the group has released scans of five types of organs—the heart, brain, kidneys, lungs, and spleen—based on donated organs from Ackermann and Jonigk’s COVID-19 autopsies in Germany and healthy “control” organs from LADAF, a Grenoble-based anatomy lab. The team has made the data, as well as fly-through movies based on the data, freely available online.
The Human Organ Atlas is rapidly growing: Another 30 organs have already been scanned, and 80 more are in various stages of preparation. Lee says that some 40 different research groups have contacted the team to learn more about the method.